scholarly journals Comparative Transcriptome Profile Analysis of Longissimus dorsi Muscle Tissues From Two Goat Breeds With Different Meat Production Performance Using RNA-Seq

2021 ◽  
Vol 11 ◽  
Author(s):  
Jiyuan Shen ◽  
Zhiyun Hao ◽  
Jiqing Wang ◽  
Jiang Hu ◽  
Xiu Liu ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Meat Quality ◽  
Differentially Expressed Genes ◽  
Collagen Fibers ◽  
Production Performance ◽  
Carcass Weight ◽  
Longissimus Dorsi ◽  
Meat Production ◽  
Rna Seq ◽  
Muscle Tissues

Carcass weight, meat quality and muscle components are important traits economically and they underpin most of the commercial return to goat producers. In this study, the Longissimus dorsi muscle tissues were collected from five Liaoning cashmere (LC) goats and five Ziwuling black (ZB) goats with phenotypic difference in carcass weight, some meat quality traits and muscle components. The histological quantitative of collagen fibers and the transcriptome profiles in the Longissimus dorsi muscle tissues were investigated using Masson-trichrome staining and RNA-Seq, respectively. The percentage of total collagen fibers in the Longissimus dorsi muscle tissues from ZB goats was less than those from LC goats, suggesting that these ZB goats had more tender meat. An average of 15,919 and 15,582 genes were found to be expressed in Longissimus dorsi muscle tissues from LC and ZB goats, respectively. Compared to LC goats, the expression levels of 78 genes were up-regulated in ZB goats, while 133 genes were down-regulated. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the differentially expressed genes (DEGs) were significantly enriched in GO terms related to the muscle growth and development and the deposition of intramuscular fat and lipid metabolism, hippo signaling pathway and Jak-STAT signaling pathway. The results provide an improved understanding of the genetic mechanisms regulating meat production performance in goats, and will help us improve the accuracy of selection for meat traits in goats using marker-assisted selection based on these differentially expressed genes obtained.

scholarly journals Identification and characterization of circRNA during muscle development in different breeds of cattle

2020 ◽  
Author(s):  
Ruili Liu ◽  
Xianxun Liu ◽  
Xuejin Bai ◽  
Chaozhu Xiao ◽  
Yajuan Dong
Keyword(s):  
Meat Quality ◽  
Muscle Development ◽  
Muscle Growth ◽  
Production Performance ◽  
Meat Production ◽  
Quality Improvements ◽  
Muscle Tissues ◽  
New Ideas ◽  
Solid Foundation ◽  
Cattle Meat

Abstract Background Black cattle are a new breed of cattle that are developed by applying modern biotechnology, such as somatic cloning, and conventional breeding methods to Luxi cattle. It is very important to study the function and regulatory mechanism of circRNAs in muscle differentiation among different breeds to improve meat quality and meat production performance and to provide new ideas for beef cattle meat quality improvements and new breed development. Therefore, the goal of this study was to sequence and identify circRNAs in muscle tissues of different breeds of cattle. We used RNA-seq to identify circRNAs in the muscles of two breeds of black cattle (Black and Luxi). Results We identified 14640 circRNAs and found 655 differentially expressed circRNAs. We also analysed the classification and characteristics of circRNAs in muscle tissue. GO and KEGG analyses were used on the parental genes of circRNAs. They were mainly involved in a variety of biological processes, such as muscle fibre development, smooth muscle cell proliferation, bone system morphogenesis, tight junctions and the MAPK, AMPK and mTOR signalling pathways. In addition, we used miRanda to predict the interactions between 15 circRNAs and 12 miRNAs. Based on the above assays, we identified circRNAs (circ0001048, circ0001103, circ0001159, circ0003719, circ0003794, circ0003721, circ0003720, circ0001519, circ0001530, circ0005060, circ0006589, circ0000181, circ0000190, circ0010558, circ0010577) that may play an important role in the regulation of muscle growth and development. Conclusion Our results provide more information about circRNAs regulating muscle development in different breeds of cattle and lay a solid foundation for future experiments.

scholarly journals PSII-22 Comparison of the meat quality traits of crossbred pigs and the Large Black pigs

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 241-242
Author(s):  
Yongjie Wang ◽  
Keshari Thakali ◽  
Sarah Shelby ◽  
Jason Apple ◽  
Yan Huang
Keyword(s):  
Meat Quality ◽  
Genomic Diversity ◽  
Longissimus Dorsi ◽  
Rna Seq ◽  
Longissimus Dorsi Muscle ◽  
A Value ◽  
Dorsi Muscle ◽  
Body Weights ◽  
C Value ◽  
Crossbred Pigs

Abstract The purpose of this study was to compare the meat quality and genomic differences between cross-bred commercial pig (CP) and domestic Large Black pig (BP). Seven cross-bred commercial pigs and eight British Large Black pigs were assigned to CP group and BP group, with initial mean body weights of 18.82±1.412 kg for CP group and 23.31±1.935 kg for BP group, P = 0.061, and fed ad libitum. The final BW of the CP at d101 was similar to the BP (130.0±8.16 kg vs. 121.1±2.80 kg, P = 0.132). However, the BP group took 108 days to reach the final BW. The ADG in the CP was higher than BP (1.102±0.0599 kg vs. 0.905±0.0138 kg, P = 0.003). The hot carcass weight of CP was higher (P < 0.01) than BP, but the backfat of BP was higher (P < 0.01) than CP. The a* value of CP was higher (P < 0.05) than BP, and the c* value of CP was tended to be higher (P < 0.10) than BP. However, the h value of BP was higher (P < 0.05) than CP. The longissimus dorsi muscle fat content of BP was higher (P < 0.05) than CP. For the fatty acid composition, the SFA and MUFA of BP were higher (P < 0.05) than CP, but the PUFA of CP was higher (P < 0.05) than BP. The metmyoglobin content of CP was tended to be higher (P < 0.10) than BP. For the meat metabolism, the oxygen consumption of longissimus dorsi muscle of BP was higher (P < 0.01) than CP. The RNA-Seq data showed that the expression of the genes related to lipid metabolism is higher in BP (fold change > 3, P < 0.05). To conclude, BP has higher meat quality, while CP has its advantages in growth performance. And the differences between these two breeds may due to the genomic diversity.

scholarly journals Identification and Characterization of Circular RNAs in Longissimus Dorsi Muscle Tissue from Two Goat Breeds using RNA-Seq

2021 ◽  
Author(s):  
Jiyuan Shen ◽  
Huimin Zhen ◽  
Lu Li ◽  
Yuting Zhang ◽  
Jiqing Wang ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Fiber ◽  
Muscle Development ◽  
Production Performance ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Longissimus Dorsi ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Fiber Size

Abstract Background: Circular RNAs (circRNAs) are a class of non-coding RNA that play crucial roles in the development of skeletal muscle. However, little is known about the role of circRNAs in caprine skeletal muscle. In this study, the muscle fiber size and expression profiles of circRNAs were compared in Longissimus dorsi muscle of Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with significant phenotypic differences in meat production performance, using hematoxylin and eosin staining and RNA-Seq, respectively.Results: The muscle fiber size in LC goats were larger than those in ZB goats (P < 0.05). A total of 10,875 circRNAs were identified and 214 of these were differentially expressed between the two caprine breeds. The authentication and expression levels of 20 circRNAs were confirmed using reverse transcriptase-polymerase chain reaction (RT-PCR) and DNA sequencing. The parent genes of differentially expressed circRNAs were mainly enriched in connective tissue development, Rap1, cGMP-PKG, cAMP and Ras signaling pathway. Some miRNAs reportedly associated with skeletal muscle development and intramuscular fat deposition would be targeted by several differentially expressed circRNAs and the most highly expressed circRNA (circ_001086).Conclusion: These results provide an improved understanding of the functions of circRNAs in skeletal muscle development of goats.

Expression profile analysis of Differentially Expressed Genes in Human Coronary Artery Endothelial Cells Induced by Serum from Kawasaki Disease: A preliminary study

2020 ◽  
Author(s):  
Xue Fan ◽  
Meng Li ◽  
Min Xiao ◽  
Cong Liu ◽  
Mingguo Xu
Keyword(s):  
Endothelial Cells ◽  
Coronary Artery ◽  
Kawasaki Disease ◽  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Healthy Children ◽  
Rna Seq ◽  
Human Coronary Artery

Abstract Background: Kawasaki disease (KD) leads to coronary artery damage and the etiology of KD is unknown. The present study was designed to explore the differentially expressed genes (DEGs) in KD serum-induced human coronary artery endothelial cells (HCAECs) by RNA-sequence (RNA-seq). Methods: HCAECs were stimulated with serum (15% (v/v)), which were collected from 20 healthy children and 20 KD patients, for 24 hours. DEGs were then detected and analyzed by RNA-seq and bioinformatics analysis. Results: The expression of SMAD1, SMAD6, CD34, CXCL1, PITX2, and APLN was validated by qPCR. 102 genes, 59 up-regulated and 43 down-regulated genes, were significantly differentially expressed in KD groups. GO enrichment analysis showed that DEGs were enriched in cellular response to cytokines, cytokine-mediated signaling pathway, and regulation of immune cells migration and chemotaxis. KEGG signaling pathway analysis showed that DEGs were mainly involved in cytokine−cytokine receptor interaction, chemokine signaling pathway, and TGF−β signaling pathway. Besides, the mRNA expression levels of SMAD1, SMAD6, CD34, CXCL1, and APLN in the KD group were significantly up-regulated compared with the normal group, whilePITX2 was significantly down-regulated. Conclusion: 102 DEGs in KD serum-induced HCAECs were identified, and six new targets were proposed as potential indicators of KD.

Castration age and growth, meat production and meat quality of Nellore male cattle

2020 ◽  
Vol 60 (5) ◽  
pp. 725
Author(s):  
R. J. Anaruma ◽  
L. G. Reis ◽  
P. E. de Felício ◽  
S. B. Pflanzer ◽  
S. Rossi ◽  
...  
Keyword(s):  
Meat Quality ◽  
Average Daily Gain ◽  
Carcass Weight ◽  
Age And Growth ◽  
Meat Production ◽  
Quality Traits ◽  
Muscle Area ◽  
Sensory Property ◽  
Meat Quality Traits

Castration in beef cattle production has been proposed to reduce sexual and aggressive behaviour, increase carcass fat deposition, and improve meat quality traits, such as tenderness and juiciness. The aim of the present study was to evaluate the effects of the age of castration on performance, subprimal yield and meat quality of Nellore cattle raised on a pasture system. A total of 24 Nellore males were raised in a grass-fed system with Brachiaria brizantha since birth until slaughter (at 30 months old). Three treatments were assigned: castration at weaning (CW); castration at 20 months old (C20); and intact bulls (NoC). Males were weighed, and muscle and fat thickness were periodically evaluated by ultrasonography. The cold carcass weight, dressing and carcass pH (pH 24), and subprimal cut weights were recorded after 24 h of chilling. Samples of Longissimus lumborum (LL) were taken to measure meat quality traits. Animals that were castrated at weaning had lower bodyweight after 10 months of age with no changes in the supplement intakes, average daily gain, hot carcass weight and cold carcass weight compared with NoC. Intact males had greater cooking losses and carcass yield compared with others, with no differences for LL pH 24 according to the treatments. The castration did not change the LL muscle area, but decreased total forequarter, chunk, shoulder and eye of round weights, and increased the back fat over LL and rump fat. Animals castrated at weaning had higher marbling compared with others. In addition, regardless of age, castration improved tenderness, increased LL total lipids and decreased moisture compared with NoC. For sensory property, steers castrated at 20 months of age had lower juiciness, and NoC had a greater global sensory property compared with steers castrated at 20 months old. In conclusion, steers castrated at weaning had lower growth rate, final bodyweight and meat production compared with intact males. However, when castration was performed at 20 months, animals did not differ in most cases from castration at weaning and NoC. Tenderness was improved by castration, but sensory traits did not differ between groups.

scholarly journals Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

2021 ◽  
Vol 12 ◽  
Author(s):  
Chun Huang ◽  
Fei Ge ◽  
Xiaoming Ma ◽  
Rongfeng Dai ◽  
Renqing Dingkao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Molecular Basis ◽  
Muscle Development ◽  
Expression Profiles ◽  
Economic Benefits ◽  
Production Performance ◽  
Differentially Expressed ◽  
Myoblast Differentiation ◽  
Longissimus Dorsi ◽  
Non Coding Rnas

Cattle-yak, as the hybrid offspring of cattle (Bos taurus) and yak (Bos grunniens), demonstrates obvious heterosis in production performance. Male hybrid sterility has been focused on for a long time; however, the mRNAs and non-coding RNAs related to muscle development as well as their regulatory networks remain unclear. The phenotypic data showed that the production performance (i.e., body weight, withers height, body length, and chest girth) of cattle-yak was significantly better than that of the yak, and the economic benefits of the cattle-yak were higher under the same feeding conditions. Then, we detected the expression profiles of the longissimus dorsi muscle of cattle-yak and yak to systematically reveal the molecular basis using the high-throughput sequencing technology. Here, 7,126 mRNAs, 791 lncRNAs, and 1,057 circRNAs were identified to be differentially expressed between cattle-yaks and yaks in the longissimus dorsi muscle. These mRNAs, lncRNA targeted genes, and circRNA host genes were significantly enriched in myoblast differentiation and some signaling pathways related to muscle development (such as HIF-1 signaling pathway and PI3K-Akt signaling pathway). We constructed a competing endogenous RNA (ceRNA) network and found that some non-coding RNAs differentially expressed may be involved in the regulation of muscle traits. Taken together, this study may be used as a reference tool to provide the molecular basis for studying muscle development.

scholarly journals Identification of critical pathways and potential therapeutic targets in Poorly differentiated duodenal papilla adenocarcinoma

2020 ◽  
Author(s):  
Yuanxiang Lu ◽  
Wensen Li ◽  
Ge Liu ◽  
Erwei Xiao ◽  
Senmao Mu ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Therapeutic Targets ◽  
Malignant Neoplasm ◽  
Differentially Expressed ◽  
High Recurrence Rate ◽  
Rna Seq ◽  
Duodenal Papilla ◽  
Ppi Network ◽  
Hub Genes

Abstract Background: Duodenal papilla carcinoma (DPC) is a rare malignancy of the gastrointestinal tract with high recurrence rate, and the pathogenesis of this highly malignant neoplasm is yet to be fully elucidated. This study aims to identify key genes to further understand the biology and pathogenesis underlying the molecular alterations driving DPC, which could be potential diagnostic or therapeutic targets.Methods: Tumor samples of three DPC patients were collected and integrating RNA-seq analysis of tumor tissues and matched normal tissues were performed to discover differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were carried out to understand the potential bio-functions of the DPC differentially expressed genes (DEGs) and protein–protein interaction (PPI) network was constructed for functional modules analysis and dentification of hub genes. Results: A total of 110 DEGs were identified from our RNA-Seq data, GO and KEGG analyses showed that the DEGs were mainly enriched in multiple cancer-related functions and pathways, such as cell proliferation, IL-17signaling pathway, Jak-STAT signaling pathway, PPAR signaling pathway. The PPI network screened out six hub genes including IL-6, LEP, LCN2, CCND1, FABP4 and MMP1, which were identified as core genes in the network and potential therapeutic targets of DPC. Discussion: The current study provides new insight into the exploration of DPC pathogenesis and the screened hub genes may serve as potential diagnostic indicator and novel therapeutic target.

scholarly journals Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kai Xing ◽  
Kejun Wang ◽  
Hong Ao ◽  
Shaokang Chen ◽  
Zhen Tan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Signaling Pathway ◽  
Meat Quality ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Mapk Signaling ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Pig Breeds

Abstract Fatness traits are important in pigs because of their implications for fattening efficiency, meat quality, reproductive performance and immunity. Songliao black pigs and Landrace pigs show important differences in production and meat quality traits, including fatness and muscle growth. Therefore, we used a high-throughput massively parallel RNA-seq approach to identify genes differentially expressed in backfat tissue between these two breeds (six pigs in each). An average of 37.87 million reads were obtained from the 12 samples. After statistical analysis of gene expression data by edgeR, a total of 877 differentially expressed genes were detected between the two pig breeds, 205 with higher expression and 672 with lower expression in Songliao pigs. Candidate genes (LCN2, CES3, DGKB, OLR1, LEP, PGM1, PCK1, ACACB, FADS1, FADS2, MOGAT2, SREBF1, PPARGC1B) with known effects on fatness traits were included among the DEGs. A total of 1071 lncRNAs were identified, and 85 of these lncRNAs were differentially expressed, including 53 up-regulated and 32 down-regulated lncRNAs, respectively. The differentially expressed genes and lncRNAs involved in glucagon signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, MAPK signaling pathway and so on. Integrated analysis potential trans-regulating or cis-regulating relation between DEGs and DE lncRNAs, suggested lncRNA MSTRG.2479.1 might regulate the expressed level of VLDLR affecting porcine fat metabolism. These results provide a number of candidate genes and lncRNAs potentially involved in porcine fat deposition and provide a basis for future research on the molecular mechanisms underlying in fat deposition.

Comparing the mRNA Expression Profile of Psoas Major and Longissimus Dorsi Muscles in Pig

2020 ◽  
Author(s):  
Yuanyuan Zhao ◽  
Guoqing Cao ◽  
Pengfei Gao ◽  
Guifang Jia ◽  
Fei Yang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Longissimus Dorsi ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Longissimus Dorsi Muscle ◽  
Qrt Pcr ◽  
Psoas Major Muscle ◽  
Types Of Muscle Fibers ◽  
Psoas Major

To explore the differentially expressed mRNAs between oxidative and glycolytic muscles, Qianbei black pigs were slaughtered and longissimus dorsi muscle (LDM) and psoas major muscle (PMM) were selected and sequenced using Illumina Hiseq TM 4000. Bioinformatics analysis and differentially expressed genes were analyzed by GO and KEGG. qRT-PCR was used to validate the RNA-seq result. As a result, 69 differentially expressed genes were identified, with 46 down regulated genes and 23 up regulated genes in LDM versus PMM, which were categorized into 44 functional groups under three GO classifications. KEGG pathway analysis revealed 20 pathways were enriched. qRT-PCR shows the expression trends of ND6, MYH7, TBX1, FOS and SLC7A5 are consist with the RNA-seq result. We speculated these five genes may involve in differentiation of muscle cells, metabolism of carbohydrate and lipid, deposits of intramuscular fat and transformation of different types of muscle fibers.

scholarly journals Transcript variants of a region on SSC15 rich in QTLs associated with meat quality in pigs

2017 ◽  
Vol 17 (3) ◽  
pp. 703-715 ◽  
Author(s):  
Katarzyna Piórkowska ◽  
Kacper Żukowski ◽  
Tomasz Szmatoła ◽  
Katarzyna Ropka-Molik ◽  
Mirosław Tyra
Keyword(s):  
Meat Quality ◽  
Chromosome Region ◽  
Variant Calling ◽  
Longissimus Dorsi ◽  
Pork Quality ◽  
Drip Loss ◽  
Gene Variants ◽  
Rna Seq ◽  
Transcriptome Profile ◽  
High Effect

Abstract A high meat percentage in the porcine carcass has been achieved as a result of selection, but it has contributed to a deterioration of pork quality. The level of intramuscular fat has significantly declined, the pork has lost its tenderness and drip loss in meat has substantially increased, which has led to a deterioration of meat flavour and its technological suitability. The recovery of good pork quality could be supported by the development of genetic markers enabling faster breeding progress. This study presents a method by using RNA-seq data that identifies new variants for a chromosome region rich in QTLs for pork quality and selects gene candidates for these traits. This work included two pig breeds: the Polish Landrace (PL) and Puławska (PUL), which differ in meat quality and fat content. The transcriptome profile was estimated for semimembranosus and longissimus dorsi muscles. Into variant calling analysis, transcripts of both muscles encoded by genes located in a region between microsatellites SW964 and SW906 (43-135.9 Mbp) in SSC15 were included. In total, 439 transcripts were searched, 2,800 gene variants were identified and 6 mutations with a high effect belonging to the frameshift variants were found (ENSSSCG00000015976, ENSSSCG00000027516, WRN and XIRP2). Moreover, several interesting significant missense variants in PDLIM3, PLCD4 and SARAF genes were detected. These genes are recommended as candidates for meat quality; however they require further investigation in an association study.

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